Examples with SingleChannelDisplayInfo qupath.lib.display.SingleChannelDisplayInfo used on opensource projects

Example 1 with SingleChannelDisplayInfo

use of qupath.lib.display.SingleChannelDisplayInfo in project qupath by qupath.

the class ExtractRegionCommand method run.

@Override
public void run() {
    QuPathViewer viewer = qupath.getViewer();
    ImageServer<BufferedImage> server = null;
    if (viewer != null)
        server = viewer.getServer();
    if (server == null)
        return;
    List<String> unitOptions = new ArrayList<>();
    unitOptions.add(PIXELS_UNIT);
    String unit = server.getPixelCalibration().getPixelWidthUnit();
    if (unit.equals(server.getPixelCalibration().getPixelHeightUnit()) && !unit.equals(PixelCalibration.PIXEL))
        unitOptions.add(unit);
    if (!unitOptions.contains(resolutionUnit))
        resolutionUnit = PIXELS_UNIT;
    ParameterList params = new ParameterList().addDoubleParameter("resolution", "Resolution", resolution, null, "Resolution at which the image will be exported, defined as the 'pixel size' in Resolution units").addChoiceParameter("resolutionUnit", "Resolution unit", resolutionUnit, unitOptions, "Units defining the export resolution; if 'pixels' then the resolution is the same as a downsample value").addBooleanParameter("includeROI", "Include ROI", includeROI, "Include the primary object defining the exported region as an active ROI in ImageJ").addBooleanParameter("includeOverlay", "Include overlay", includeOverlay, "Include any objects overlapping the exported region as ROIs on an ImageJ overlay").addBooleanParameter("doTransforms", "Apply color transforms", doTransforms, "Optionally apply any color transforms when sending the pixels to ImageJ").addBooleanParameter("doZ", "All z-slices", doZ, "Optionally include all slices of a z-stack").addBooleanParameter("doT", "All timepoints", doT, "Optionally include all timepoints of a time series");
    // params.setHiddenParameters(unitOptions.size() <= 1, "resolutionUnit");
    params.setHiddenParameters(server.nZSlices() == 1, "doZ");
    params.setHiddenParameters(server.nTimepoints() == 1, "doT");
    if (!Dialogs.showParameterDialog("Send region to ImageJ", params))
        return;
    // Parse values
    resolution = params.getDoubleParameterValue("resolution");
    resolutionUnit = (String) params.getChoiceParameterValue("resolutionUnit");
    includeROI = params.getBooleanParameterValue("includeROI");
    includeOverlay = params.getBooleanParameterValue("includeOverlay");
    doTransforms = params.getBooleanParameterValue("doTransforms");
    doZ = params.getBooleanParameterValue("doZ");
    doT = params.getBooleanParameterValue("doT");
    // Calculate downsample
    double downsample = resolution;
    if (!resolutionUnit.equals(PIXELS_UNIT))
        downsample = resolution / (server.getPixelCalibration().getPixelHeight().doubleValue() / 2.0 + server.getPixelCalibration().getPixelWidth().doubleValue() / 2.0);
    // Color transforms are (currently) only applied for brightfield images - for fluorescence we always provide everything as unchanged as possible
    List<ChannelDisplayInfo> selectedChannels = new ArrayList<>(viewer.getImageDisplay().selectedChannels());
    List<ChannelDisplayInfo> channels = doTransforms && !selectedChannels.isEmpty() ? selectedChannels : null;
    if (channels != null)
        server = ChannelDisplayTransformServer.createColorTransformServer(server, channels);
    // Loop through all selected objects
    Collection<PathObject> pathObjects = viewer.getHierarchy().getSelectionModel().getSelectedObjects();
    if (pathObjects.isEmpty())
        pathObjects = Collections.singletonList(viewer.getHierarchy().getRootObject());
    List<ImagePlus> imps = new ArrayList<>();
    for (PathObject pathObject : pathObjects) {
        if (Thread.currentThread().isInterrupted() || IJ.escapePressed())
            return;
        int width, height;
        if (pathObject == null || !pathObject.hasROI()) {
            width = server.getWidth();
            height = server.getHeight();
        } else {
            Rectangle bounds = AwtTools.getBounds(pathObject.getROI());
            width = bounds.width;
            height = bounds.height;
        }
        RegionRequest region;
        ROI roi = pathObject == null ? null : pathObject.getROI();
        if (roi == null || PathObjectTools.hasPointROI(pathObject)) {
            region = RegionRequest.createInstance(server.getPath(), downsample, 0, 0, server.getWidth(), server.getHeight(), viewer.getZPosition(), viewer.getTPosition());
        } else
            region = RegionRequest.createInstance(server.getPath(), downsample, roi);
        // region = RegionRequest.createInstance(server.getPath(), downsample, pathObject.getROI(), viewer.getZPosition(), viewer.getTPosition());
        // Minimum size has been removed (v0.2.0-m4); returned regions should be at least 1x1 pixels
        // if (region.getWidth() / downsample < 8 || region.getHeight() / downsample < 8) {
        // DisplayHelpers.showErrorMessage("Send region to ImageJ", "The width & height of the extracted image must both be >= 8 pixels");
        // continue;
        // }
        // Calculate required z-slices and time-points
        int zStart = doZ ? 0 : region.getZ();
        int zEnd = doZ ? server.nZSlices() : region.getZ() + 1;
        int tStart = doT ? 0 : region.getT();
        int tEnd = doT ? server.nTimepoints() : region.getT() + 1;
        long nZ = zEnd - zStart;
        long nT = tEnd - tStart;
        int bytesPerPixel = server.isRGB() ? 4 : server.getPixelType().getBytesPerPixel() * server.nChannels();
        double memory = ((long) width * height * nZ * nT * bytesPerPixel) / (downsample * downsample);
        // TODO: Perform calculation based on actual amount of available memory
        long availableMemory = GeneralTools.estimateAvailableMemory();
        if (memory >= availableMemory * 0.95) {
            logger.error("Cannot extract region {} - estimated size is too large (approx. {} MB)", pathObject, GeneralTools.formatNumber(memory / (1024.0 * 1024.0), 2));
            Dialogs.showErrorMessage("Send region to ImageJ error", "Selected region is too large to extract - please selected a smaller region or use a higher downsample factor");
            continue;
        }
        if (memory / 1024 / 1024 > 100) {
            if (pathObjects.size() == 1 && !Dialogs.showYesNoDialog("Send region to ImageJ", String.format("Attempting to extract this region is likely to require > %.2f MB - are you sure you want to continue?", memory / 1024 / 1024)))
                return;
        }
        // We should switch to the event dispatch thread when interacting with ImageJ
        try {
            ImagePlus imp;
            PathObjectHierarchy hierarchy = viewer.getHierarchy();
            OverlayOptions options = viewer.getOverlayOptions();
            if (zEnd - zStart > 1 || tEnd - tStart > 1) {
                // TODO: Handle overlays
                imp = IJTools.extractHyperstack(server, region, zStart, zEnd, tStart, tEnd);
                if (includeROI && roi != null) {
                    Roi roiIJ = IJTools.convertToIJRoi(roi, imp.getCalibration(), region.getDownsample());
                    imp.setRoi(roiIJ);
                }
                if (includeOverlay) {
                    Overlay overlay = new Overlay();
                    for (int t = tStart; t < tEnd; t++) {
                        for (int z = zStart; z < zEnd; z++) {
                            RegionRequest request2 = RegionRequest.createInstance(region.getPath(), region.getDownsample(), region.getX(), region.getY(), region.getWidth(), region.getHeight(), z, t);
                            var regionPredicate = PathObjectTools.createImageRegionPredicate(request2);
                            Overlay temp = IJExtension.extractOverlay(hierarchy, request2, options, p -> p != pathObject && regionPredicate.test(p));
                            if (overlay == null)
                                overlay = temp;
                            for (int i = 0; i < temp.size(); i++) {
                                Roi roiIJ = temp.get(i);
                                roiIJ.setPosition(-1, z + 1, t + 1);
                                overlay.add(roiIJ);
                            }
                        }
                    }
                    if (overlay != null && overlay.size() > 0)
                        imp.setOverlay(overlay);
                }
            } else if (includeOverlay)
                imp = IJExtension.extractROIWithOverlay(server, pathObject, hierarchy, region, includeROI, options).getImage();
            else
                imp = IJExtension.extractROIWithOverlay(server, pathObject, null, region, includeROI, options).getImage();
            // Set display ranges if we can
            if (viewer != null && imp instanceof CompositeImage) {
                var availableChannels = viewer.getImageDisplay().availableChannels().stream().filter(c -> c instanceof SingleChannelDisplayInfo).map(c -> (SingleChannelDisplayInfo) c).collect(Collectors.toList());
                CompositeImage impComp = (CompositeImage) imp;
                if (availableChannels.size() == imp.getNChannels()) {
                    for (int c = 0; c < availableChannels.size(); c++) {
                        var channel = availableChannels.get(c);
                        imp.setPosition(c + 1, 1, 1);
                        impComp.setDisplayRange(channel.getMinDisplay(), channel.getMaxDisplay());
                    }
                    imp.setPosition(1);
                }
            } else if (selectedChannels.size() == 1 && imp.getType() != ImagePlus.COLOR_RGB) {
                // Setting the display range for non-RGB images can give unexpected results (changing pixel values)
                var channel = selectedChannels.get(0);
                imp.setDisplayRange(channel.getMinDisplay(), channel.getMaxDisplay());
            }
            imps.add(imp);
        } catch (IOException e) {
            Dialogs.showErrorMessage("Send region to ImageJ", e);
            return;
        }
    }
    // Show all the images we've got
    if (!imps.isEmpty()) {
        SwingUtilities.invokeLater(() -> {
            boolean batchMode = Interpreter.batchMode;
            // Try to start an ImageJ instance, and return if this fails
            try {
                ImageJ ij = IJExtension.getImageJInstance();
                if (ij == null)
                    return;
                ij.setVisible(true);
                // Make sure we aren't in batch mode, so that image will display
                Interpreter.batchMode = false;
                for (ImagePlus imp : imps) {
                    imp.show();
                }
            } finally {
                Interpreter.batchMode = batchMode;
            }
        });
    }
}

Example 2 with SingleChannelDisplayInfo

use of qupath.lib.display.SingleChannelDisplayInfo in project qupath by qupath.

the class ChannelDisplayTransformServer method readBufferedImage.

@Override
public BufferedImage readBufferedImage(final RegionRequest request) throws IOException {
    // Transform the pixels, if required
    BufferedImage img = getWrappedServer().readBufferedImage(request);
    int width = img.getWidth();
    int height = img.getHeight();
    WritableRaster raster = null;
    float[] pxFloat = null;
    int b = 0;
    for (ChannelDisplayInfo channel : channels) {
        if (channel instanceof SingleChannelDisplayInfo) {
            if (raster == null) {
                SampleModel model = new BandedSampleModel(DataBuffer.TYPE_FLOAT, width, height, nChannels());
                raster = Raster.createWritableRaster(model, null);
            }
            if (raster.getTransferType() == DataBuffer.TYPE_FLOAT) {
                pxFloat = ((SingleChannelDisplayInfo) channel).getValues(img, 0, 0, width, height, pxFloat);
                raster.setSamples(0, 0, width, height, b, pxFloat);
                b++;
            } else {
                logger.error("Unable to apply color transform " + channel.getName() + " - incompatible with previously-applied transforms");
            }
        } else if (channels.size() == 1) {
            int[] rgb = channel.getRGB(img, null, false);
            img.setRGB(0, 0, width, height, rgb, 0, width);
            return img;
        } else {
            logger.error("Cannot apply requested color transforms! Must either be a single RGB transform, or one or more single-channel transforms");
        }
    }
    if (colorModel == null)
        colorModel = ColorModelFactory.createColorModel(PixelType.FLOAT32, channels.size(), false, channels.stream().mapToInt(c -> {
            Integer color = c.getColor();
            if (color == null)
                color = ColorTools.packRGB(255, 255, 255);
            return color;
        }).toArray());
    return new BufferedImage(colorModel, raster, false, null);
}